Profile Posts Awards
Show
all questions tools blogs news tutorials forum answers comments
Showing : all
0
votes
0
replies
7.6k
views
Comment: C: Samtofastq: Net.Sf.Picard.Picardexception: "Found N Unpaired Mates "
updated 4.4 years ago by 43k • written 9.6 years ago by ▴ 160
0
votes
0
replies
2.8k
views
Comment: Comment: how to export RNA-seq reads which mapped to genes?
updated 3.1 years ago by 43k • written 9.5 years ago by ▴ 160
0
votes
0
replies
2.8k
views
Comment: Comment: how to export RNA-seq reads which mapped to genes?
updated 3.1 years ago by 43k • written 9.5 years ago by ▴ 160
0
votes
0
replies
2.8k
views
Comment: Comment: how to export RNA-seq reads which mapped to genes?
updated 3.1 years ago by 43k • written 9.5 years ago by ▴ 160
0
votes
1
reply
2.8k
views
Comment: Comment: how to export RNA-seq reads which mapped to genes?
updated 3.1 years ago by 43k • written 9.5 years ago by ▴ 160
0
votes
1
reply
2.1k
views
total-hits-norm and compatible-hits-norm default setting different in Cufflinks and Cuffdiff
RNA-Seq Cufflinks Cuffdiff
6.1 years ago by trakhtenberg ▴ 160
6
votes
2
replies
3.5k
views
Comparing Fpkm values from samples processed in same or different runs using tophat/cufflinks
rna-seq
updated 7.0 years ago by 20 • written 9.7 years ago by ▴ 160
0
votes
0
replies
2.2k
views
Comment: C: Does upper-quartile normalization in Cuffdiff also normalizes by transcript leng
7.9 years ago by trakhtenberg ▴ 160
0
votes
0
replies
2.9k
views
Upper-quartile normalization option for Cufflinks and Cuffdiff
Cufflinks Cuffdiff Upper-quartile normalization
7.9 years ago by trakhtenberg ▴ 160
1
vote
2
replies
2.2k
views
Does upper-quartile normalization in Cuffdiff also normalizes by transcript length?
RNA-Seq Cuffdiff Upper-quartile normalization
updated 7.9 years ago by 13k • written 7.9 years ago by ▴ 160
5
votes
4
replies
3.5k
views
How to identify with Tophat maximum number of uniquely aligned reads by allowing mismatches only conditionally?
RNA-Seq
updated 2.3 years ago by 43k • written 9.6 years ago by ▴ 160
0
votes
1
reply
3.7k
views
GOseq and KEGG pathways analysis for mouse RNA-seq
KEGG RNA-Seq GOseq
updated 23 months ago by 43k • written 9.1 years ago by ▴ 160
1
vote
1
reply
2.3k
views
PWF from GOseq to adjust q-value in Cuffdiff
GOseq RNA-Seq gene length bias
updated 23 months ago by 43k • written 9.1 years ago by ▴ 160
0
votes
0
replies
2.8k
views
Comment: Comment: how to export RNA-seq reads which mapped to genes?
updated 3.1 years ago by 43k • written 9.5 years ago by ▴ 160
0
votes
0
replies
2.8k
views
Comment: Comment: how to export RNA-seq reads which mapped to genes?
updated 3.1 years ago by 43k • written 9.5 years ago by ▴ 160
0
votes
2
replies
2.8k
views
Comment: Comment: how to export RNA-seq reads which mapped to genes?
updated 3.1 years ago by 43k • written 9.5 years ago by ▴ 160
3
votes
16
replies
2.8k
views
how to export RNA-seq reads which mapped to genes?
RNA-Seq
updated 2.2 years ago by 43k • written 9.5 years ago by ▴ 160
0
votes
1
reply
2.8k
views
Comment: Comment: how to export RNA-seq reads which mapped to genes?
updated 3.1 years ago by 43k • written 9.5 years ago by ▴ 160
0
votes
6
replies
4.9k
views
Converting BAM to Fastq with HTSlib htscmd
Fastq Bam2Fastq Tophat BAM HTSlib
updated 2.3 years ago by 43k • written 9.6 years ago by ▴ 160
0
votes
1
reply
3.3k
views
sorting merged GTFs for Tophat/Cufflinks pipeline
GTF Cufflinks
9.6 years ago by trakhtenberg ▴ 160
0
votes
0
replies
8.0k
views
Comment: C: How to reduce reads in fastq, bam, bed files in a random manner?
9.6 years ago by trakhtenberg ▴ 160
0
votes
0
replies
1.6k
views
Which flagstat output categories are passed by Tophat to Cufflinks for analysis?
flagstat Cufflinks Tophat
updated 2.3 years ago by 43k • written 9.6 years ago by ▴ 160
0
votes
0
replies
4.8k
views
Comment: Comment: Picard error Illegal Mate State in converting BAM to Fastq
updated 2.3 years ago by 43k • written 9.6 years ago by ▴ 160
0
votes
0
replies
4.9k
views
Comment: C: Converting BAM to Fastq with HTSlib htscmd
9.6 years ago by trakhtenberg ▴ 160
4
votes
3
replies
4.8k
views
Picard error Illegal Mate State in converting BAM to Fastq
Picard SamToFastq BamToFastq
updated 2.3 years ago by 43k • written 9.6 years ago by ▴ 160
0
votes
0
replies
9.0k
views
Answer: A: Picard Exception: Illegal Mate State
9.6 years ago by trakhtenberg ▴ 160
0
votes
1
reply
49k
views
Comment: Comment: Fastq Splitter For Paired End Reads
updated 2.3 years ago by 43k • written 9.6 years ago by ▴ 160
0
votes
0
replies
3.5k
views
Comment: Comment: How to identify with Tophat maximum number of uniquely aligned reads by allowing
updated 2.3 years ago by 43k • written 9.6 years ago by ▴ 160
0
votes
1
reply
3.5k
views
Comment: Comment: How to identify with Tophat maximum number of uniquely aligned reads by allowing
updated 2.3 years ago by 43k • written 9.6 years ago by ▴ 160
0
votes
0
replies
10k
views
Comment: Comment: Extracting from tophat outputs reads pairs and splice-junctions with a single be
updated 2.3 years ago by 43k • written 9.6 years ago by ▴ 160
0
votes
1
reply
10k
views
Comment: Comment: Extracting from tophat outputs reads pairs and splice-junctions with a single be
updated 2.3 years ago by 43k • written 9.6 years ago by ▴ 160
11
votes
10
replies
10k
views
Extracting from tophat outputs reads pairs and splice-junctions with a single best match
TOPHAT RNA-Seq
updated 2.3 years ago by 43k • written 9.7 years ago by ▴ 160
0
votes
2
replies
2.6k
views
Comment: C: How to convert strand-specific reads to not-strand-specific format?
9.7 years ago by trakhtenberg ▴ 160
4
votes
5
replies
2.6k
views
How to convert strand-specific reads to not-strand-specific format?
RNA-Seq
updated 2.3 years ago by 43k • written 9.7 years ago by ▴ 160
9
votes
9
replies
8.0k
views
6 follow
How to reduce reads in fastq, bam, bed files in a random manner?
RNA-Seq
updated 2.3 years ago by 43k • written 9.7 years ago by ▴ 160
0
votes
0
replies
11k
views
Comment: Comment: tophat output files containing the reads which mapped uniquely as a pair
updated 2.3 years ago by 43k • written 9.7 years ago by ▴ 160
4
votes
2
replies
11k
views
tophat output files containing the reads which mapped uniquely as a pair
TOPHAT RNA-Seq
updated 2.3 years ago by 43k • written 9.7 years ago by ▴ 160
0
votes
0
replies
4.5k
views
Comment: C: Identifying polyA tail sequences for predicted novel transcripts using STAR/Cuff
9.7 years ago by trakhtenberg ▴ 160
0
votes
0
replies
4.5k
views
Comment: C: Identifying polyA tail sequences for predicted novel transcripts using STAR/Cuff
9.7 years ago by trakhtenberg ▴ 160
0
votes
0
replies
1.3k
views
comprehensive mouse GTF for discovery of novel transcripts? Beyond GENCODE M3
RNA-Seq
updated 9.7 years ago by 20 • written 9.7 years ago by ▴ 160
0
votes
1
reply
4.5k
views
Comment: Comment: Identifying polyA tail sequences for predicted novel transcripts using STAR/Cuff
updated 2.4 years ago by 43k • written 9.7 years ago by ▴ 160
0
votes
1
reply
4.5k
views
Comment: Comment: Identifying polyA tail sequences for predicted novel transcripts using STAR/Cuff
updated 2.4 years ago by 43k • written 9.7 years ago by ▴ 160
5
votes
8
replies
4.5k
views
Identifying polyA tail sequences for predicted novel transcripts using STAR/Cufflinks
RNA-Seq
updated 2.4 years ago by 43k • written 9.7 years ago by ▴ 160
0
votes
0
replies
1.8k
views
Best annotation GTFs for transcript detection vs novel transcript discovery
RNA-Seq
updated 2.4 years ago by 43k • written 9.7 years ago by ▴ 160
0
votes
0
replies
3.7k
views
Comment: C: Are polyA tails filtered at some step of tophat/cufflinks processing or this inf
9.7 years ago by trakhtenberg ▴ 160
0
votes
0
replies
3.7k
views
Comment: C: Are polyA tails filtered at some step of tophat/cufflinks processing or this inf
9.7 years ago by trakhtenberg ▴ 160
0
votes
1
reply
3.7k
views
Comment: Comment: Are polyA tails filtered at some step of tophat/cufflinks processing or this inf
updated 2.4 years ago by 43k • written 9.7 years ago by ▴ 160
8
votes
6
replies
3.7k
views
Are polyA tails filtered at some step of tophat/cufflinks processing or this information is retained?
RNA-Seq
updated 2.4 years ago by 43k • written 9.7 years ago by ▴ 160
0
votes
0
replies
3.5k
views
Comment: C: Comparing Fpkm values from samples processed in same or different runs using top
9.7 years ago by trakhtenberg ▴ 160
49 results • Page 1 of 1
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6